Feature Extraction
The engine of the feature extraction module is GSCtool, a genomic descriptor we developed previously. GSCtool counts the number of single nucleotide polymorphisms (SNPs) located in a gene region based on genomic general feature format (GFF3) and variant call format (VCF).
GSCtool
IRGSP-1.0, Williams82, Zm-B73 are the most commonly used reference genomes for rice, soybean, and maize genome analysis, respectively. You can upload SNPs variant detection files (snp.vcf.gz) for these reference genomes for these species, and this module will complete the GSCtool feature characterisation of the uploaded individuals or populations and return the result files.
If you need to perform GSCtool feature extraction on the variant detection results with special reference genomes, you can download GSCtool and follow the instructions to complete GSCtool feature extraction locally.
